tjh.dev
nixpkgs mirror (for testing)
github.com/NixOS/nixpkgs
nix
1{
2 lib,
3 stdenv,
4 fetchurl,
5 jre,
6 makeWrapper,
7}:
8
9stdenv.mkDerivation rec {
10 pname = "varscan";
11 version = "2.4.6";
12
13 src = fetchurl {
14 url = "https://github.com/dkoboldt/varscan/raw/master/VarScan.v${version}.jar";
15 sha256 = "sha256-6CcjC0epbKsDXFxxeOUImSGh4cjR5INqawL/iOOkwqs=";
16 };
17
18 nativeBuildInputs = [ makeWrapper ];
19 buildInputs = [ jre ];
20
21 dontUnpack = true;
22
23 installPhase = ''
24 mkdir -p $out/libexec/varscan
25 cp $src $out/libexec/varscan/varscan.jar
26 mkdir -p $out/bin
27 makeWrapper ${jre}/bin/java $out/bin/varscan --add-flags "-jar $out/libexec/varscan/varscan.jar"
28 '';
29
30 meta = with lib; {
31 description = "Variant calling and somatic mutation/CNV detection for next-generation sequencing data";
32 # VarScan 2 is free for non-commercial use by academic,
33 # government, and non-profit/not-for-profit institutions. A
34 # commercial version of the software is available, and licensed
35 # through the Office of Technology Management at Washington
36 # University School of Medicine.
37 license = licenses.unfree;
38 homepage = "https://github.com/dkoboldt/varscan";
39 sourceProvenance = with sourceTypes; [ binaryBytecode ];
40 maintainers = with maintainers; [ jbedo ];
41 platforms = platforms.all;
42 };
43
44}